CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
helpString += "The cluster.classic command should be in the following format: \n";
helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
- helpString += "The acceptable cluster methods are furthest, nearest, weighted and average. If no method is provided then furthest is assumed.\n\n";
+ helpString += "The acceptable cluster methods are furthest, nearest, weighted and average. If no method is provided then average is assumed.\n";
return helpString;
}
catch(exception& e) {
convert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; }
+ temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
hard = m->isTrue(temp);
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
sim = m->isTrue(temp);
method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "furthest"; }
+ if (method == "not found") { method = "average"; }
if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) {
if (method == "furthest") { tag = "fn"; }